The 21 year-old midfielder, who is now set to jet off to Egypt, to help South Africa try and qualify for the Tokyo 2020 Olympic games, placed a fine header past Ricardo Goss in stoppage time as Wits ultimately paid the price for wasting a host of opportunities.
SuperSport also did put up a fine defensive display, with Ronwen Williams superb in goal, and young Luke Fleurs excelling in the heart of the defence.
Williams was called into action as early as the 7th minute, as Sameehg Doutie fired in a shot from the edge of the box that the Bafana goalkeeper did superbly to tip round the post.
At the other end, Bradley Grobler fired over the bar for SuperSport, but it was Wits who did most of the attacking, with Gift Motupa given a chance by Gavin Hunt after netting four times on the weekend in the Caf Confederation Cup.
Motupa, however, did not have his shooting boots on this time, wasting two or three presentable opportunities to give the Clever Boys the lead.
Elias Pelembe also missed a good second half opportunity for Wits, who ultimately paid the price, as SuperSport netted late to leapfrog them into third in the table.